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Modeling the language of life – Deep Learning Protein Sequences
Open accessPreprint — published as 10.1186/s12859-019-3220-8 · Paper page
Abstract
Background: One common task in Computational Biology is the prediction of aspects of protein function and structure from their amino acid sequence. For 26 years, most state-of-the-art approaches toward this end have been marrying machine learning and evolutionary information. The retrieval of related proteins from ever growing sequence databases is becoming so time-consuming that the analysis of entire proteomes becomes challenging. On top, evolutionary information is less powerful for small families, e.g. for proteins from the Dark Proteome . Results: We introduce a novel way to represent protein sequences as continuous vectors ( embeddings ) by using the deep bi-directional model ELMo taken from natural language processing (NLP). The model has effectively captured the biophysical properties of protein sequences from unlabeled big data (UniRef50). After training, this knowledge is transferred to single protein sequences by predicting relevant sequence features. We refer to these new embeddings as SeqVec ( Seq uence-to- Vec tor) and demonstrate their effectiveness by training simple convolutional neural networks on existing data sets for two completely different prediction tasks. At the per-residue level, we significantly improved secondary structure (for NetSurfP-2.0 data set: Q3=79%±1, Q8=68%±1) and disorder predictions (MCC=0.59±0.03) over methods not using evolutionary information. At the per-protein level, we predicted subcellular localization in ten classes (for DeepLoc data set: Q10=68%±1) and distinguished membrane-bound from water-soluble proteins (Q2= 87%±1). All results built upon the embeddings gained from the new tool SeqVec neither explicitly nor implicitly using evolutionary information. Nevertheless, it improved over some methods using such information. Where the lightning-fast HHblits needed on average about two minutes to generate the evolutionary information for a target protein, SeqVec created the vector representation on average in 0.03 seconds. Conclusion: We have shown that transfer learning can be used to capture biochemical or biophysical properties of protein sequences from large unlabeled sequence databases. The effectiveness of the proposed approach was showcased for different prediction tasks using only single protein sequences. SeqVec embeddings enable predictions that outperform even some methods using evolutionary information. Thus, they prove to condense the underlying principles of protein sequences. This might be the first step towards competitive predictions based only on single protein sequences. Availability: SeqVec: https://github.com/mheinzinger/SeqVec Prediction server: https://embed.protein.properties
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Elnaggar, A., Heinzinger, M., Dallago, C., Rehawi, G., Wang, Y., Jones, L., Gibbs, T., Feher, T., Angerer, C., Steinegger, M., et al. (2022) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2021.3095381 · Cited by 2,329
Self-citationProteinBERT: a universal deep-learning model of protein sequence and function
Brandes, N., Ofer, D., Peleg, Y., Rappoport, N., & Linial, M. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac020 · Cited by 1,009
Metadata
- Authors
- Heinzinger, M., Elnaggar, A., Wang, Y., Dallago, C., Nechaev, D., Matthes, F., & Rost, B.
- Affiliations
- Technical University of Munich (DE)
- Leibniz Supercomputing Centre (DE)
- Corresponding author
- Heinzinger, Michael
- Venue
- BMC Bioinformatics
- Publisher
- openRxiv
- Published
- 2019-04-19
- Volume
- 20
- Issue
- 1
- Pages
- 723-723
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC6918593
- OpenAlex
- W2995514860
- Cited by
- 606
- References
- 105
- Citations by year
- 2026: 53 · 2025: 103 · 2024: 115 · 2023: 117 · 2022: 99 · 2021: 83 · 2020: 29 · 2019: 7
- FWCI
- 18.03
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
- Columbia Academic Commons (Columbia University)
- Funders
- Alexander von Humboldt-Stiftung
- Nvidia
- Deutsche Forschungsgemeinschaft (DFG-GZ: RO1320/4-1, RO1320/4‐1)
- Bundesministerium für Bildung und Forschung
- Leibniz-Gemeinschaft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- protein sequence embeddings, ELMo, transfer learning, protein function prediction, protein structure prediction, secondary structure prediction, subcellular localization prediction, membrane proteins, dark proteome, metaproteomics, microbiome analysis
- MeSH terms
- Machine Learning, Amino Acid Sequence, Natural Language Processing, Proteins, Neural Networks, Computer, Sequence Analysis, Computational Biology, Databases, Nucleic Acid, Databases, Protein, Proteomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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